chr10-59331232-T-A

Variant names:

• chr10-59331232-T-A
• rs166924
• NM_198215.4:c.325-7126A>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198215.4(FAM13C):​c.325-7126A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,990 control chromosomes in the GnomAD database, including 16,305 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (16305 hom., cov: 32)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

Genes affected

FAM13C (HGNC:19371): (family with sequence similarity 13 member C)

LOC102724778 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM13C	NM_198215.4	c.325-7126A>T		intron_variant	Intron 3 of 13	ENST00000618804.5	NP_937858.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM13C	ENST00000618804.5	c.325-7126A>T		intron_variant	Intron 3 of 13	1	NM_198215.4	ENSP00000481854.1

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68274 AN: 151872 Hom.: 16281 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.427

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.450 AC: 68342 AN: 151990 Hom.: 16305 Cov.: 32 AF XY: 0.448 AC XY: 33273 AN XY: 74288

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.426

Alfa AF: 0.253 Hom.: 557

Bravo AF: 0.460

Asia WGS AF: 0.501 AC: 1738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs166924; hg19: chr10-61090992;